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Author SHA1 Message Date
Ghislain Vaillant
cb9e02e554 gnu: Add python-sshfs. 
* gnu/packages/python-xyz.scm (python-sshfs): New variable.

Change-Id: I22ea5d608f8b02d584dd2d8318d2142e898e629f
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-30 12:42:46 +00:00
Ghislain Vaillant
d2550caf8e gnu: Add python-mock-ssh-server. 
* gnu/packages/python-xyz.scm (python-mock-ssh-server): New variable.

Change-Id: Id5ab44d812fb6e0d8758961e81e4659e7c215823
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-30 12:41:56 +00:00
Sharlatan Hellseher
44772b3bc8 gnu: idr: Switch to pyproject. 
* gnu/packages/bioinformatics.scm (idr)[build-system]: Switch to
pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: Ib6811a399b4c531f119bcef23b3216ff70c2d5eb
 2025-10-30 11:31:10 +00:00
Sharlatan Hellseher
64dac23e32 gnu: python-deeptoolsintervals: Switch to pyproject. 
* gnu/packages/bioinformatics.scm (python-deeptoolsintervals):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-pytest and python-setuptools.

Change-Id: I2f95aa4f526f879d9407d7625834f389e384bc39
 2025-10-30 11:29:10 +00:00
Sharlatan Hellseher
6896332787 gnu: python-twobitreader: Update to 3.1.9. 
* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.9.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?>: Enable.
[native-inputs]: Remove python-sphinx; add python-pytest and
python-setuptools.

Change-Id: I1c8d450611f1a3f3d271606bb744dd24c5f60d4d
 2025-10-30 11:16:21 +00:00
Sharlatan Hellseher
6b6a3c6cba gnu: bwa-meth: Update to 0.2.9. 
* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.9.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?>: No tests.
[inputs]: Add python-toolshed.
[native-inputs]: Remove python-toolshed; add python-setuptools.

Change-Id: Ib3544054943af904f4acea0a899f86ef66e7a47d
 2025-10-30 11:04:51 +00:00
Sharlatan Hellseher
075dc6ec28 gnu: python-fastalite: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (python-fastalite): Update to 0.4.1.
[source]: Switch to git-fetch providing test data.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?>: Enable.
<test-backend>: Use 'unittest.
<phases>: Add set-version.
[native-inputs]: Add python-setuptools.

Change-Id: Ie6659208edb37995303cf332e3b985a89d5e8d39
 2025-10-30 10:52:20 +00:00
Sharlatan Hellseher
b68eb98be0 gnu: python-cmseq: Fix build. 
* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73):
Rename variable to python-bcbio-gff-for-python-cmseq and pin to 0.6.9
version which is the last one compatible with python-biopython-1.73.
(python-cmseq)[propagated-inputs]: Remove
python-bcbio-gff/biopython-1.73; add python-bcbio-gff-for-python-cmseq.
[native-inputs]: Add python-setuptools.

Change-Id: Id7c37f8f34058648506645ce07c2a89dfcea2067
 2025-10-30 10:25:16 +00:00
Sharlatan Hellseher
898721e174 gnu: python-ega-download-client: Update to 5.2.1. 
* gnu/packages/bioinformatics.scm (python-ega-download-client): Update to 5.2.1.
[arguments]: Use G-Expressions.
<test-flags>: Rework skipped tests and ignored tests files
generating very larg test files (up to 150GiB) which may affect the CI
or user's machine.
[native-inputs]: Remove python-coverage and python-wheel; add
nss-certs-for-test.

Change-Id: Ic91c65e548e27d6c57396000233b6e5f5949554c
 2025-10-30 09:53:54 +00:00
Maxim Cournoyer
a4acb04cbd Revert "gnu: Add zstd-final." 
This reverts commit e945001f04.
 2025-10-30 16:20:05 +09:00
Maxim Cournoyer
84c92de611 Revert "gnu: %final-inputs: Use zstd-final." 
This reverts commit 75d24fbfef.
 2025-10-30 16:20:04 +09:00
Maxim Cournoyer
e983b65c8d Revert "gnu: Add pkg-config-final." 
This reverts commit 72a99ff1a7.
 2025-10-30 16:20:04 +09:00
Maxim Cournoyer
d93bb701a0 Revert "gnu: binutils-final: Enable zstd support." 
This reverts commit 0c1de511f8.
 2025-10-30 16:20:03 +09:00
Maxim Cournoyer
267c864822 Revert "gnu: binutils: Fix indentation." 
This reverts commit afe80d2a63.
 2025-10-30 16:20:03 +09:00
Maxim Cournoyer
b6323d3f1a Revert "gnu: binutils: Do not compress debug sections." 
This reverts commit 3410d8bdc8.
 2025-10-30 16:20:02 +09:00
Maxim Cournoyer
95b64bbaee Revert "gnu: binutils: Enable zstd compression." 
This reverts commit 16f0f497cd.
 2025-10-30 16:20:01 +09:00
Maxim Cournoyer
4801cb6f8f Revert "gnu: binutils-boot0: Refactor arguments." 
This reverts commit 6f229017f5.
 2025-10-30 16:20:01 +09:00
Maxim Cournoyer
63d395cf61 Revert "gnu: binutils: Use zstd compression level 19." 
This reverts commit 87a23070f2.
 2025-10-30 16:20:00 +09:00
Maxim Cournoyer
6cb1b4ec4c Revert "gnu: Add dwz." 
This reverts commit 88945309b2.
 2025-10-30 16:20:00 +09:00
Maxim Cournoyer
1842df46c1 Revert "gnu: Add elfutils-final." 
This reverts commit 7d5721de9a.
 2025-10-30 16:20:00 +09:00
Maxim Cournoyer
d1b94d1e70 Revert "gnu: Add xxhash-final." 
This reverts commit c97232c4d3.
 2025-10-30 16:19:59 +09:00
Maxim Cournoyer
29eb3783ae Revert "gnu: Add dwz-final." 
This reverts commit 4e2a5b27dd.
 2025-10-30 16:19:59 +09:00
Maxim Cournoyer
a49affc02b Revert "gnu %final-inputs: Add dwz-final." 
This reverts commit 86b4c975e9.
 2025-10-30 16:19:58 +09:00
Maxim Cournoyer
3d2256dce6 Revert "build/gnu: Do not attempt to strip Guile byte-compiled files." 
This reverts commit 2ac2a4877d.
 2025-10-30 16:19:58 +09:00
Maxim Cournoyer
d65646baf2 Revert "build/gnu: Add a compress-debug-info phase." 
This reverts commit 0688d27174.
 2025-10-30 16:19:57 +09:00
Maxim Cournoyer
c0a4052c6a Revert "gnu: xz: Update to 5.8.1." 
This reverts commit 6dec2fbccb.
 2025-10-30 16:19:57 +09:00
Maxim Cournoyer
8d6ad7edc5 Revert "gnu: readline: Update to 8.3." 
This reverts commit 9cceaad44a.
 2025-10-30 16:19:57 +09:00
Maxim Cournoyer
775c3efadb Revert "gnu: bash: Update to 5.3." 
This reverts commit 1d73b616a9.
 2025-10-30 16:19:56 +09:00
Maxim Cournoyer
7bd0d6a038 Revert "gnu: ed: Update to 1.22.2." 
This reverts commit 7fc35b3465.
 2025-10-30 16:19:56 +09:00
Maxim Cournoyer
b4a2979cbc Revert "gnu: m4: Update to 1.4.20." 
This reverts commit 81fcd98bac.
 2025-10-30 16:19:55 +09:00
Maxim Cournoyer
6113501327 Revert "gnu: flex: Apply a patch fixing a non-deterministic build failure." 
This reverts commit 6faa102a04.
 2025-10-30 16:19:55 +09:00
Maxim Cournoyer
96818c1a7c Revert "gnu: flex: Move bison-for-tests input to native inputs." 
This reverts commit c334cf0bb9.
 2025-10-30 16:19:54 +09:00
Maxim Cournoyer
902127d92b Revert "gnu: libtool: Update to 2.5.4." 
This reverts commit da8179893f.
 2025-10-30 16:19:54 +09:00
Maxim Cournoyer
8593227f40 Revert "gnu: acl: Update to 2.3.2." 
This reverts commit 6c3e5f1665.
 2025-10-30 16:19:53 +09:00
Maxim Cournoyer
db74afaab8 Revert "gnu: gettext-minimal: Update to 0.26." 
This reverts commit e6f3c37fa2.
 2025-10-30 16:19:53 +09:00
Maxim Cournoyer
09b0ee0f24 Revert "gnu: help2man: Update to 1.49.3." 
This reverts commit 1fc884a374.
 2025-10-30 16:19:53 +09:00
Maxim Cournoyer
663e92bb32 Revert "gnu: autoconf: Update to 2.72." 
This reverts commit db051f5715.
 2025-10-30 16:19:52 +09:00
Maxim Cournoyer
6878d0da2f Revert "gnu: hunspell: Update to 1.7.2." 
This reverts commit 36a90a1a04.
 2025-10-30 16:19:52 +09:00
Maxim Cournoyer
3ae5c9f2a7 Revert "syscalls: Add mmap support." 
This reverts commit e1994a0214.
 2025-10-30 16:19:51 +09:00
Maxim Cournoyer
0f39db9c19 Revert "Use mmap for the elf parser, reducing memory usage." 
This reverts commit 2c1fe0df11.
 2025-10-30 16:19:50 +09:00
Maxim Cournoyer
9d60fdf6a2 Revert "elf: Remove bundled Guile source." 
This reverts commit 11cf5b2fe4.
 2025-10-30 16:19:49 +09:00
Maxim Cournoyer
e0148efc7f Revert "gnu: gcc-mesboot: Raise default timeout via property." 
This reverts commit f4768a9a9d.
 2025-10-30 16:19:47 +09:00
Maxim Cournoyer
f4768a9a9d gnu: gcc-mesboot: Raise default timeout via property. 
It was found to time out in the CI after 21600 seconds.

* gnu/packages/commencement.scm (gcc-mesboot) [properties]: New field.

Change-Id: Idec8a668f4f15e9ed3712d505b82704260b4295d
 2025-10-30 16:13:03 +09:00
Maxim Cournoyer
11cf5b2fe4 elf: Remove bundled Guile source. 
This module has been included in Guile as (system vm elf) since around version
2.1.

* guix/elf.scm: Delete file.
* CODEOWNERS: De-register module.
* Makefile.am (MODULES): Likewise.
* etc/teams.scm (core): Likewise.
* gnu/build/linux-modules.scm: Adjust imports.
* gnu/packages/gnuzilla.scm (icecat-minimal) [modules]: Likewise.
* gnu/packages/librewolf.scm (librewolf): Likewise.
* gnu/packages/sequoia.scm (sequoia): Likewise.
* gnu/packages/tor-browsers.scm (make-torbrowser): Likewise.
* gnu/packages/version-control.scm (hg-commitsigs): Likewise.
* guix/build/debug-link.scm: Likewise.
* guix/build/gnu-build-system.scm: Likewise.
* guix/build/gremlin.scm: Likewise.
* guix/build/meson-build-system.scm: Likewise.
* guix/grafts.scm (graft-derivation/shallow): Likewise.
* guix/scripts/pack.scm (wrapped-package): Likewise.
* tests/debug-link.scm: ("elf-debuglink", "set-debuglink-crc"): Likewise.
* tests/gremlin.scm: Likewise.
* guix/build-system/gnu.scm (%default-gnu-imported-modules): Remove (guix elf).

Change-Id: I86ac4237fdd820a6b54dc0fe7a7d10403a290ef9
 2025-10-30 16:13:03 +09:00
Maxim Cournoyer
2c1fe0df11 Use mmap for the elf parser, reducing memory usage. 
The `file->bytevector' new procedure uses a memory mapped bytevector, so
parsing the ELF file reads only the sections needed, not the whole file.

* guix/scripts/pack.scm (wrapped-package): Use file->bytevector.
* guix/build/gremlin.scm (file-dynamic-info): Likewise.
(validate-needed-in-runpath): Likewise.
(strip-runpath): Likewise, and write to bytevector directly, avoiding a port.
(set-file-runpath): Likewise.
* tests/gremlin.scm (read-elf): Delete procedure.
("elf-dynamic-info-needed, executable"): Use file-dynamic-info.
("strip-runpath"): Likewise.
("elf-dynamic-info-soname"): Likewise.
 guix/build/debug-link.scm (set-debuglink-crc): Use file->bytevector.
* tests/debug-link.scm (read-elf): Delete procedure.
("elf-debuglink"): Rename to...
("elf-debuglink, no .gnu_debuglink section"): ... this.
("elf-debuglink", "set-debuglink-crc"): Use external store, and adjust to use
file->bytevector.
* gnu/packages/gnuzilla.scm (icecat-minimal) [#:phases]
{build-sandbox-whitelist}: Use `file-runpath'.
* gnu/packages/librewolf.scm (librewolf): Likewise.

Fixes: <https://issues.guix.gnu.org/59365>
Fixes: #1262
Change-Id: I43b77ed0cdc38994ea89d3d401e0d136aa6b187a
 2025-10-30 16:13:03 +09:00
Maxim Cournoyer
e1994a0214 syscalls: Add mmap support. 
* guix/build/syscalls.scm (PROT_NONE, PROT_READ, PROT_WRITE, PROT_EXEC)
(PROT_SEM, MAP_SHARED, MAP_PRIVATE, MAP_FAILED)
(MS_ASYNC, MS_INVALIDATE, MS_SYNC)
(%mmap-guardian, %unmapped-bytevectors): New variables.
(unmapped-bytevector?, pump-mmap-guardian, %mmap, mmap, %munmap, munmap)
(%msync, msync): New procedures.
* guix/build/io.scm: New file.
* Makefile.am: Register it.
* tests/syscalls.scm (strace-output): New variable.
("mmap and munmap", "file->bytevector, reading", "file->bytevector, writing")
("manual munmap does not lead to double free"): New tests.

Change-Id: I19ec687899eda635559e91200dd8d98669b0e35f
 2025-10-30 16:13:03 +09:00
Maxim Cournoyer
36a90a1a04 gnu: hunspell: Update to 1.7.2. 
* gnu/packages/hunspell.scm (hunspell): Update to 1.7.2.
[native-inputs]: Add gettext-minimal.

Change-Id: Ibdc4378c90a1a1fbad0134f6d7744fad2aac3d86
 2025-10-30 16:13:03 +09:00
Maxim Cournoyer
db051f5715 gnu: autoconf: Update to 2.72. 
* gnu/packages/autotools.scm (autoconf): Point to autoconf-2.72.
* gnu/packages/dbm.scm (bdb-4.8) [native-inputs]: Replace autoconf with
autoconf-2.69.

Change-Id: Ifa0fdd7bab21aa585e729f4e6ccf8ab15b0f73f3
 2025-10-30 16:13:03 +09:00
Maxim Cournoyer
1fc884a374 gnu: help2man: Update to 1.49.3. 
* gnu/packages/man.scm (help2man): Update to 1.49.3.

Change-Id: I9fc62620e89ca1f66b5ec402b19c639425ee5ecb
 2025-10-30 16:13:03 +09:00
Maxim Cournoyer
e6f3c37fa2 gnu: gettext-minimal: Update to 0.26. 
* gnu/packages/gettext.scm (gettext-minimal): Update to 0.26.

Change-Id: I7d594b6a89a7e12a5e0ed2da7875407800e33415
 2025-10-30 16:13:02 +09:00